Fig. 1b

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Fig 1c

Genes detected

Fig 1d

Sample Correlation Matrix

Fig 1e-h

PCA Plots (using all genes)

3d plot

PC Median Heatmaps

Figure 1-1

Distribution of mean TPM by stage

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Figure 1-2

PCA Matrix Plot

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Figure 1-3

DETCT Sample QC plot

Figure 1-4

DETCT PCA

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Figure 3

Fig3A

Max Stage Clusters TPM heatmap

ZFA enrichment

Figure 3-1

Orthologues of Named/Unnamed genes

Named Genes

Unnamed Genes

Figure 3-2

Effect of Normalisation on cluster 11

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Figure 4

Cluster Chromosome Count Expected log2FE Adjusted.pvalue
Cluster023 Chr1 9 2.25 2.00 1.161e-02
Cluster004 Chr4 129 47.29 1.45 7.434e-24
Cluster022 Chr4 14 5.03 1.48 1.156e-02
Cluster037 Chr4 23 3.35 2.78 9.033e-14
Cluster084 Chr4 9 1.48 2.61 1.659e-04
Cluster074 Chr12 8 0.48 4.05 6.337e-07

Table showing clusters with significant chr enrichments (adjusted p-value < 0.05 and log2 fold change > 1).

Chr 4 Zinc Finger Genes

Cluster Freq
4 Cluster004 120
37 Cluster037 18
22 Cluster022 14
84 Cluster084 6

Table showing the numbers of chromosome 4 zinc finger genes in the biolayout clusters (more than 5 in a cluster).

Chr 4 ZnF enrichment

The table below shows the clusters with enrichments significantly larger than expected by chance for the chromosome 4 zinc finger genes.

Cluster Category Count Expected log2FE pvalue adjusted.pvalue
Cluster004 Chr4ZnF 120 7.87 3.93 1.203e-101 6.015e-101
Cluster022 Chr4ZnF 14 0.84 4.06 7.471e-14 3.735e-13
Cluster037 Chr4ZnF 18 0.56 5.01 1.270e-23 6.349e-23
Cluster084 Chr4ZnF 6 0.25 4.61 8.588e-08 4.294e-07

Table showing clusters with significant enrichments (adjusted p-value < 0.05).

Fig4A

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Fig4C - NLR genes tpm heatmap

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Fig4D - Chr22 Znf genes tpm heatmap

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Fig4E - Chr4 tpm heatmap

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Fig4F-G - histograms of ZnF/NLR genes on chr 4

Histogram showing the distribution of genes in clusters 4, 22, 37 and 84.

Histogram showing the distribution of NLR genes on chromosome 4 (binwidth = 5 Mb).

Figure 4-2

histograms of ZnF genes on chr 4, split by cluster

Histogram showing the distribution of genes in clusters 4, 22, 37 and 84, split by cluster.

Regional expression

Figure 4-3A

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Figure 4-3 B-G

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Figure 5

Fig5A

Pearson histogram (Paralogues)

Histogram of Pearson coefficients between paralogous gene pairs (binwidth = 0.1)

Fig5B

Pearson histogram (random sample)

Histogram of Pearson coefficients of a random selection of 3000 genes pairs.

Fig5C

top10/bottom10 tpm heatmap

Fig5D-G

scatterplots/point based expression profiles

Fig.6C

Count bar chart by Stage

Session Info

## R version 3.3.1 (2016-06-21)
## Platform: x86_64-apple-darwin13.4.0 (64-bit)
## Running under: OS X 10.11.6 (El Capitan)
## 
## locale:
## [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
## 
## attached base packages:
##  [1] grid      stats4    parallel  stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] rgl_0.97.0                 qvalue_2.4.2              
##  [3] genefilter_1.54.2          DESeq2_1.12.4             
##  [5] SummarizedExperiment_1.2.3 htmlTable_1.9             
##  [7] biomaRt_2.28.0             Rgraphviz_2.16.0          
##  [9] gridExtra_2.2.1            topGO_2.24.0              
## [11] SparseM_1.7                GO.db_3.3.0               
## [13] graph_1.50.0               cba_0.2-18                
## [15] proxy_0.4-16               RColorBrewer_1.1-2        
## [17] plyr_1.8.4                 GenomicFeatures_1.24.5    
## [19] AnnotationDbi_1.34.4       Biobase_2.32.0            
## [21] GenomicRanges_1.24.2       GenomeInfoDb_1.8.3        
## [23] IRanges_2.6.1              S4Vectors_0.10.3          
## [25] BiocGenerics_0.18.0        scales_0.4.1              
## [27] reshape2_1.4.2             ggplot2_2.1.0             
## [29] rprojroot_1.2              knitr_1.15.1              
## 
## loaded via a namespace (and not attached):
##  [1] jsonlite_1.0            splines_3.3.1          
##  [3] shiny_1.0.0             Formula_1.2-1          
##  [5] highr_0.6               latticeExtra_0.6-28    
##  [7] Rsamtools_1.24.0        yaml_2.1.14            
##  [9] RSQLite_1.1-2           backports_1.0.5        
## [11] lattice_0.20-34         digest_0.6.12          
## [13] XVector_0.12.1          checkmate_1.8.1        
## [15] colorspace_1.2-6        httpuv_1.3.3           
## [17] htmltools_0.3.5         Matrix_1.2-6           
## [19] XML_3.98-1.5            zlibbioc_1.18.0        
## [21] xtable_1.8-2            BiocParallel_1.6.6     
## [23] annotate_1.50.0         nnet_7.3-12            
## [25] mime_0.5                survival_2.40-1        
## [27] magrittr_1.5            memoise_1.0.0          
## [29] evaluate_0.10           foreign_0.8-66         
## [31] tools_3.3.1             data.table_1.10.0      
## [33] matrixStats_0.50.2      stringr_1.1.0          
## [35] munsell_0.4.3           locfit_1.5-9.1         
## [37] cluster_2.0.5           Biostrings_2.40.2      
## [39] RCurl_1.95-4.8          htmlwidgets_0.8        
## [41] labeling_0.3            bitops_1.0-6           
## [43] base64enc_0.1-3         rmarkdown_1.3          
## [45] gtable_0.2.0            DBI_0.5-1              
## [47] R6_2.2.0                GenomicAlignments_1.8.4
## [49] rtracklayer_1.32.2      Hmisc_4.0-2            
## [51] stringi_1.1.1           Rcpp_0.12.9            
## [53] geneplotter_1.50.0      rpart_4.1-10           
## [55] acepack_1.4.1